Package: puremoe 1.1.0

Jason Timm

puremoe: Unified Retrieval of 'PubMed' and 'NIH' Literature Data

Access a variety of 'PubMed' data through a single, user-friendly interface, including abstracts, bibliometrics from 'iCite', pubtations from 'PubTator3', and full-text records from 'PMC'.

Authors:Jason Timm [aut, cre]

puremoe_1.1.0.tar.gz
puremoe_1.1.0.zip(r-4.7)puremoe_1.1.0.zip(r-4.6)puremoe_1.1.0.zip(r-4.5)
puremoe_1.1.0.tgz(r-4.6-any)puremoe_1.1.0.tgz(r-4.5-any)
puremoe_1.1.0.tar.gz(r-4.7-any)puremoe_1.1.0.tar.gz(r-4.6-any)
puremoe_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
puremoe/json (API)
NEWS

# Install 'puremoe' in R:

install.packages('puremoe', repos = c('https://jaytimm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jaytimm/puremoe/issues

Pkgdown/docs site:https://jaytimm.github.io

Datasets:

data_mesh_frequencies - MeSH Descriptor Frequencies Across PubMed

On CRAN:

pubmed-central pubmed-parser

5.38 score 3 stars 4 scripts 451 downloads 11 exports 37 dependencies

Last updated from:87e7800fdf. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	160
source / vignettes	OK	248
linux-release-x86_64	OK	154
macos-release-arm64	OK	131
macos-oldrel-arm64	OK	153
windows-devel	OK	91
windows-release	OK	90
windows-oldrel	OK	88
wasm-release	OK	130

Exports:citation_network citation_snowball data_mesh_thesaurus data_mesh_trees endpoint_info get_records pmid_to_ftp pmid_to_pmc pubtator_cooccurrence pubtator_sentences search_pubmed

Dependencies:askpass cli cpp11 curl data.table generics glue httr jsonlite lattice lifecycle lubridate magrittr Matrix mime openssl pbapply pillar pkgconfig R6 rappdirs rentrez rlang rvest selectr slam stringi stringr sys textpress textshape tibble timechange utf8 vctrs XML xml2

Citation Snowballing for Literature Discovery

Rendered fromcitation-snowball.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-06-02
Started: 2026-06-02

Getting Started

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-06-02
Started: 2026-03-18

MeSH Tables

Rendered frommesh-search.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-06-02
Started: 2026-03-18

PubTator Sentence Mapping

Rendered frompubtator-sentences.Rmdusingknitr::rmarkdownon Jun 03 2026.

Last update: 2026-06-02
Started: 2026-06-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build a Citation Network from an iCite Corpus	citation_network
Expand a PMID Corpus via One-Hop iCite Citation Snowballing	citation_snowball
MeSH Descriptor Frequencies Across PubMed	data_mesh_frequencies
Download and Combine 'MeSH' and Supplemental Thesauruses	data_mesh_thesaurus
Download and Load 'MeSH' Trees Data	data_mesh_trees
Get Information About Available Endpoints	endpoint_info
Retrieve Data from 'NLM'/'PubMed' databases Based on PMIDs	get_records
Convert PubMed IDs (PMIDs) to PMC IDs and Full-Text URLs	pmid_to_ftp
Convert PubMed IDs (PMIDs) to PMC IDs	pmid_to_pmc
Count Entity Co-occurrence from Sentence-Mapped PubTator3 Annotations	pubtator_cooccurrence
Map PubTator3 Annotations to Abstract Sentences	pubtator_sentences
Search 'PubMed' Records	search_pubmed